Analysis of the algorithm: From rankings to backup genes.

Ranking section

Table 1. Performance summary for every kernel and net before integration.

Net Kernel tpr_down_ci_0.95 tpr_up_ci_0.95 fpr_down_ci_0.95 fpr_up_ci_0.95 f
biological_process ct 1 1 1 1 0.904761904761905
biological_process el 1 1 1 1 0.904761904761905
biological_process ka 1 1 1 1 0.904761904761905
biological_process rf 1 1 1 1 0.904761904761905
cellular_component ct 0.792672413793104 1 0.416666666666667 1 0.919354838709677
cellular_component el 1 1 1 1 0.90625
cellular_component ka 0.724137931034483 1 0.416666666666667 0.916666666666667 0.935483870967742
cellular_component rf 0.724137931034483 1 0.414583333333335 1 0.926829268292683
disease ct 0.363636363636364 1 0 1 0.956521739130435
disease el 0.181818181818182 1 0 1 0.956521739130435
disease ka 1 1 0.333333333333333 1 0.936170212765957
disease rf 0.318181818181818 1 0 1 0.956521739130435
gene_TF ct 1 1 0.6 1 0.918032786885246
gene_TF el 1 1 1 1 0.918032786885246
gene_TF ka 1 1 1 1 0.918032786885246
gene_TF node2vec 0.427678571428572 1 0.4 1 0.933333333333333
gene_TF rf 1 1 1 1 0.918032786885246
gene_hgncGroup ct 0.407407407407407 1 0.666666666666667 1 0.905982905982906
gene_hgncGroup el 1 1 1 1 0.9
gene_hgncGroup ka 1 1 1 1 0.9
gene_hgncGroup rf 1 1 1 1 0.9
molecular_function ct 1 1 1 1 0.90625
molecular_function el 1 1 0.916666666666667 1 0.90625
molecular_function ka 1 1 1 1 0.90625
molecular_function rf 1 1 1 1 0.90625
pathway ct 0.288461538461538 1 0.272727272727273 1 0.91588785046729
pathway el 1 1 1 1 0.904347826086957
pathway ka 1 1 1 1 0.904347826086957
pathway node2vec 1 1 1 1 0.904347826086957
pathway rf 1 1 1 1 0.904347826086957
phenotype ct 0.0434782608695652 1 0.166666666666667 1 0.92
phenotype el 0.130434782608696 1 0.166666666666667 1 0.92
phenotype ka 1 1 0.333333333333333 1 0.884615384615384
phenotype rf 0.0434782608695652 1 0.166666666666667 1 0.92
protein_interaction ct 1 1 1 1 0.909090909090909
protein_interaction el 1 1 1 1 0.909090909090909
protein_interaction ka 1 1 0.916666666666667 1 0.909090909090909
protein_interaction node2vec 1 1 1 1 0.909090909090909
protein_interaction rf 1 1 1 1 0.909090909090909

Table 2. Performance summary for every kernel after integration

Integration Kernel tpr_down_ci_0.95 tpr_up_ci_0.95 fpr_down_ci_0.95 fpr_up_ci_0.95 f
integration_mean_by_presence ct 1 1 1 1 0.909090909090909
integration_mean_by_presence el 1 1 1 1 0.909090909090909
integration_mean_by_presence ka 1 1 0.916666666666667 1 0.909090909090909
integration_mean_by_presence node2vec 1 1 1 1 0.909090909090909
integration_mean_by_presence rf 1 1 1 1 0.909090909090909
mean ct 1 1 1 1 0.909090909090909
mean el 1 1 1 1 0.909090909090909
mean ka 1 1 0.916666666666667 1 0.909090909090909
mean node2vec 1 1 1 1 0.909090909090909
mean rf 1 1 1 1 0.909090909090909

ROC plots of non integrated kernels

ROC plots of integrated kernels